Complexity Digest 2011.23
2011/11/25
Editor-in-Chief: Carlos Gershenson
Founding Editor: Gottfried Mayer
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Content
- Optimization of brain and life performance: Striving for playing at the top for the long run, arXiv
- Lynn Margulis 1938-2011 "Gaia Is A Tough Bitch", Edge.org
- Robust Signal Processing in Living Cells, PLoS Comput Biol
- Urban lead, Nature Geoscience
- Living in Living Cities, arXiv
- Robin Ince: Science versus wonder?, TED.com
- Cynthia Kenyon: Experiments that hint of longer lives, TED.com
- Discovering Network Structure Beyond Communities, Scientific Reports
- Modelling Epidemics on Networks, arXiv
- The role of sex separation in neutral speciation, arXiv
- Electricity Now and When, Science
- Electrical Energy Storage for the Grid: A Battery of Choices, Science
- Smart Swarms of Bacteria Inspire Robotics: Adaptable Decision-Making Found in Bacteria Communities, ScienceDaily
- The age of the megacity, Nature Geoscience
- Evolutionary Time Travel, Science
- Division of labour and the evolution of multicellularity, arXiv
- Environmental effects of information and communications technologies, Nature
- Peer-review in a world with rational scientists: Toward selection of the average, Eur. Phys. J. B
- Image characterization and classification by physical complexity, Complexity
- Natural Complexity, Computational Complexity and Depth, arXiv
- Rational Choice, Context Dependence, and the Value of Information in European Starlings (Sturnus vulgaris), Science
- Collective Animal Behavior from Bayesian Estimation and Probability Matching, PLoS Comput Biol
- Memristive excitable cellular automata, arXiv
- Book Announcements
- The Price of Fish: A New Approach to Wicked Economics and Better Decisions, Nicholas Brealey Publishing
- Who's in Charge?: Free Will and the Science of the Brain, Ecco
- Language and Music as Cognitive Systems, Oxford University Press
- Brilliant Mistakes: Finding Success on the Far Side of Failure, Wharton Digital Press
- Bioinformatics for Biologists, Cambridge University Press
- Computational Complexity: Theory, Techniques, and Applications, Springer
- Links & Snippets
- Other Publications
- Event Announcements
- Video Announcements
- Other Announcements
Optimization of brain and life performance: Striving for playing at the top for the long run, arXiv 
Abstract: In this essay written with my students and collaborators in mind, I share simple recipes that are easy and often fun to put in practice and that make a big difference in one's life. The seven guiding principles are: (1) sleep, (2) love and sex, (3) deep breathing and daily exercises, (4) water and chewing, (5) fruits, unrefined products, food combination, vitamin D and no meat, (6) power foods, (7) play, intrinsic motivation, positive psychology and will. These simple laws are based on an integration of evolutionary thinking, personal experimentation, and evidence from experiments reported in the scientific literature. I develop their rationality, expected consequences and describe briefly how to put them in practice. I hope that professionals and the broader public may also find some use for it, as I have seen already the positive impacts on some of my students.
Lynn Margulis 1938-2011 "Gaia Is A Tough Bitch", Edge.org
Excerpt: Biologist Lynn Margulis died on November 22nd. She stood out from her colleagues in that she would have extended evolutionary studies nearly four billion years back in time. Her major work was in cell evolution, in which the great event was the appearance of the eukaryotic, or nucleated, cell â€" the cell upon which all larger life-forms are based. Nearly forty-five years ago, she argued for its symbiotic origin: that it arose by associations of different kinds of bacteria. Her ideas were generally either ignored or ridiculed when she first proposed them; symbiosis in cell evolution is now considered one of the great scientific breakthroughs.
Robust Signal Processing in Living Cells, PLoS Comput Biol
Excerpt: Cellular signaling networks have to function reliably and with high fidelity in an uncertain environment. In this paper, we investigate the topological principles to achieve such robust signal processing in living cells. Specifically, we identify the topological organizing principles that enable a signaling network to keep the stationary intracellular concentrations of certain molecules, such as active signaling compounds, within tightly defined bounds â€" despite conditions of uncertainty and in the face of multiple perturbations. We demonstrate that an appropriate topological organization renders the output of the pathway invariant against a large class of possible detrimental fluctuations (…)
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Excerpt: Humanity has evolved into an urban species. Already, more than half the planet's population lives in cities and this fraction is expected to rise to 70% by 2070. The speed and scale of urban growth poses significant social, economic and environmental challenges, such as ensuring that the 10 million or so inhabitants of megacities have access to adequate supplies of food and clean water each day. But urban areas also concentrate and foster human ingenuity. Innovative solutions to the problems of the twenty-first century, ranging from climate change and poverty to energy supply, are most likely to be thought up in the stimulating environments that make up urban centres. In this way, cities could help to mitigate the ill effects of an ever-crowding planet.
See Also: Nature Geoscience Focus on Cities, November 2011 Volume 4 No 11 pp729-812
- Source: Urban lead, Editorial, DOI: 10.1038/ngeo1322, Nature Geoscience 4, 733, 2011/10/31
Living in Living Cities, arXiv
Abstract: This paper presents and overview of current and potential applications of living technology to urban problems. Living technology can be described as technology that exhibits the core features of living systems. These features can be useful to solve dynamic problems. In particular, urban problems concerning mobility, logistics, telecommunications, governance, safety, sustainability, and society and culture are presented, while solutions involving living technology are reviewed. Finally, the usefulness of describing cities as living systems is discussed.
Robin Ince: Science versus wonder?, TED.com
About this talk: Does science ruin the magic of life? In this grumpy but charming monologue, Robin Ince makes the argument against. The more we learn about the astonishing behavior of the universe -- the more we stand in awe.
Cynthia Kenyon: Experiments that hint of longer lives, TED.com
About this talk: What controls aging? Biochemist Cynthia Kenyon has found a simple genetic mutation that can double the lifespan of a simple worm, C. elegans. The lessons from that discovery, and others, are pointing to how we might one day significantly extend youthful human life.
Discovering Network Structure Beyond Communities, Scientific Reports
Abstract: To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving network structure remains a challenging problem. Here we overcome this difficulty by combining the visual pattern recognition ability of humans with the high processing speed of computers to develop an exploratory method for discovering groups of nodes characterized by common network properties, including but not limited to communities of densely connected nodes. Without any prior information about the nature of the groups, the method simultaneously identifies the number of groups, the group assignment, and the properties that define these groups. The results of applying our method to real networks suggest the possibility that most group structures lurk undiscovered in the fast-growing inventory of social, biological, and technological networks of scientific interest.
Modelling Epidemics on Networks, arXiv
Abstract: Infectious disease remains, despite centuries of work to control and mitigate its effects, a major problem facing humanity. This paper reviews the mathematical modelling of infectious disease epidemics on networks, starting from the simplest Erdos-Renyi random graphs, and building up structure in the form of correlations, heterogeneity and preference, paying particular attention to the links between random graph theory, percolation and dynamical systems representing transmission. Finally, the problems posed by networks with a large number of short closed looks are discussed.
The role of sex separation in neutral speciation, arXiv
Abstract: Neutral speciation mechanisms based on isolation by distance and sexual selection, termed topopatric, have recently been shown to describe the observed patterns of abundance distributions and species-area relationships. Previous works have considered this type of process only in the context of hermaphrodic populations. In this work we extend a hermaphroditic model of topopatric speciation to populations where individuals are explicitly separated into males and females. We show that for a particular carrying capacity speciation occurs under similar conditions, but the number of species generated decreases as compared to the hermaphroditic case. Evolution results in fewer species having more abundant populations.
Electricity Now and When, Science
Excerpt: Whether it started with falling water or with the burning or radioactive decomposition of fuels, creating and delivering electrical power used to be a straightforward process of trying to balance generation, distribution, and demand at a reasonable cost to end users. Peak power requirements have grown, as has the size of the fluctuations between daily maximum and minimum requirements. Very little capacity exists for storing electricity, but an increased reliance on renewable sources, especially solar and wind power, will require better solutions to electricity storage to cope with their intermittent nature.
- Source: Electricity Now and When, Marc Lavine, Phillip Szuromi, Robert Coontz, DOI: 10.1126/science.334.6058.921, Science Vol. 334 no. 6058 p. 921, 2011/11/18
Electrical Energy Storage for the Grid: A Battery of Choices, Science
Abstract: The increasing interest in energy storage for the grid can be attributed to multiple factors, including the capital costs of managing peak demands, the investments needed for grid reliability, and the integration of renewable energy sources. Although existing energy storage is dominated by pumped hydroelectric, there is the recognition that battery systems can offer a number of high-value opportunities, provided that lower costs can be obtained. The battery systems reviewed here include sodium-sulfur batteries that are commercially available for grid applications, redox-flow batteries that offer low cost, and lithium-ion batteries whose development for commercial electronics and electric vehicles is being applied to grid storage.
Smart Swarms of Bacteria Inspire Robotics: Adaptable Decision-Making Found in Bacteria Communities, ScienceDaily
Excerpts: researchers at Tel Aviv University have developed a computational model that better explains how bacteria move in a swarm -- and this model can be applied to human-made technologies, including computers, artificial intelligence, and robotics. (…) Studying the principles of bacteria navigation will allow researchers to design a new generation of smart robots that can form intelligent swarms, aid in the development of medical micro-robots used to diagnose or distribute medications in the body, or "de-code" systems used in social networks and throughout the Internet to gather information on consumer behaviors
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Excerpt: (…) we remain largely ignorant of what cities really are. The good news is that enormous enthusiasm and effort has started to pour into issues of urban security, sustainability and prosperity, and that a new breed of data-driven, interdisciplinary research into cities is emerging. One such example is Living in the Endless City, a polyphonic collection of essays that examine issues such as governance, violence, inequality, climate change and transportation in three of the world's developing megacities: Mumbai, São Paulo and Istanbul.
- Source: The age of the megacity, LuĂs M. A. Bettencourt, DOI: 10.1038/ngeo1299, Nature Geoscience 4, 733, 2011/10/31
Evolutionary Time Travel, Science
Summary: With clever and challenging lab experiments, researchers are forcing species to become multicellular, develop new energy sources, and start having sex.
- Source: Evolutionary Time Travel, Elizabeth Pennisi, DOI: 10.1126/science.334.6058.893, Science Vol. 334 no. 6058 pp. 893-895, 2011/11/18
Division of labour and the evolution of multicellularity, arXiv
Excerpt: Understanding the emergence and evolution of multicellularity and cellular differentiation is a core problem in biology. We develop a quantitative model that shows that a multicellular form emerges from genetically identical unicellular ancestors when the compartmentalization of poorly compatible physiological processes into component cells of an aggregate produces a fitness advantage. (…)
Environmental effects of information and communications technologies, Nature
Excerpt: The digital revolution affects the environment on several levels. Most directly, information and communications technology (ICT) has environmental impacts through the manufacturing, operation and disposal of devices and network equipment, but it also provides ways to mitigate energy use, for example through smart buildings and teleworking. At a broader system level, ICTs influence economic growth and bring about technological and societal change. Managing the direct impacts of ICTs is more complex than just producing efficient devices, owing to the energetically expensive manufacturing process, and the increasing proliferation of devices needs to be taken into account.
Peer-review in a world with rational scientists: Toward selection of the average, Eur. Phys. J. B
Excerpt: It is widely believed that one of the virtues of peer review is that it provides a self-regulating selection mechanism for scientific work, papers and projects. Peer review as a selection mechanism is hard to evaluate in terms of its efficiency. Serious efforts to understand its strengths and weaknesses have not yet lead to conclusive answers. In theory peer review works if the involved parties (editors and referees) conform to a set of requirements, such as love for high quality science, objectiveness, and absence of biases, nepotism, friend and clique networks, selfishness, etc. If these requirements are violated, what is the effect on the selection of high quality work? We study this question with a simple agent based model. (…)
Image characterization and classification by physical complexity, Complexity
Excerpt: We present a method for estimating the complexity of an image based on Bennett's concept of logical depth. Bennett identified logical depth as the appropriate measure of organized complexity, and hence as being better suited to the evaluation of the complexity of objects in the physical world. Its use results in a different, and in some sense a finer characterization than is obtained through the application of the concept of Kolmogorov complexity alone. We use this measure to classify images by their information content. The method provides a means for classifying and evaluating the complexity of objects by way of their visual representations. (…)
Natural Complexity, Computational Complexity and Depth, arXiv
Abstract: Depth is a complexity measure for natural systems of the kind studied in statistical physics and is defined in terms of computational complexity. Depth quantifies the length of the shortest parallel computation required to construct a typical system state or history starting from simple initial conditions. The properties of depth are discussed and it is compared to other complexity measures. Depth can only be large for systems with embedded computation.
Rational Choice, Context Dependence, and the Value of Information in European Starlings (Sturnus vulgaris), Science
Abstract: Both human and nonhuman decision-makers can deviate from optimal choice by making context-dependent choices. Because ignoring context information can be beneficial, this is called a “less-is-more effect.” The fact that organisms are so sensitive to the context is thus paradoxical and calls for the inclusion of an ecological perspective. In an experiment with starlings, adding cues that identified the context impaired performance in simultaneous prey choices but improved it in sequential prey encounters, in which subjects could reject opportunities in order to search instead in the background. Because sequential prey encounters are likely to be more frequent in nature, storing and using contextual information appears to be ecologically rational on balance by conditioning acceptance of each opportunity to the relative richness of the background, even if this causes context-dependent suboptimal preferences in (less-frequent) simultaneous choices. In ecologically relevant scenarios, more information seems to be more.
Collective Animal Behavior from Bayesian Estimation and Probability Matching, PLoS Comput Biol
Excerpt: Animals need to act on uncertain data and with limited cognitive abilities to survive. It is well known that our sensory and sensorimotor processing uses probabilistic estimation as a means to counteract these limitations. Indeed, the way animals learn, forage or select mates is well explained by probabilistic estimation. Social animals have an interesting new opportunity since the behavior of other members of the group provides a continuous flow of indirect information about the environment. This information can be used to improve their estimations of environmental factors. Here we show that this simple idea can derive basic interaction rules that animals use for decisions in social contexts. In particular, we show that the patterns of choice of Gasterosteus aculeatus correspond very well to probabilistic estimation using the social information. (…)
Memristive excitable cellular automata, arXiv
Excerpt: The memristor is a device whose resistance changes depending on the polarity and magnitude of a voltage applied to the device's terminals. We design a minimalistic model of a regular network of memristors using structurally-dynamic cellular automata.
Book Announcements
The Price of Fish: A New Approach to Wicked Economics and Better Decisions, Nicholas Brealey Publishing
Summary: The world is faced with a series of vicious and apparently insurmountable difficulties, chief among them unstable financial markets, rapidly diminishing resources and an eco-system that is becoming dangerously volatile. This book examines in a unique way the world s most abiding and wicked problems, all of which are characterized by a set of messy, circular, aggressive and peculiarly long-term problems. Looking to the models developed by quantum physicists, the authors aim to blend four streams choice, economics, systems and evolution in a combination they believe is the key to making better decisions
Who's in Charge?: Free Will and the Science of the Brain, Ecco
Summary: The father of cognitive neuroscience offers a provocative argument against the common belief that our lives are wholly determined by physical processes and we are therefore not responsible for our actions. Neuroscientist Michael S. Gazzaniga in this provocative book based on his Gifford Lectures, proposes that the mind, which is somehow generated by the physical processes of the brain, �constrains� the brain just as cars are constrained by the traffic they create. (...)
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Summary: The past 15 years have witnessed an increasing interest in the comparative study of language and music as cognitive systems. Language and music are uniquely human traits, so it is not surprising that this interest spans practically all branches of cognitive science, including psychology, computer science, linguistics, cognitive neuroscience, and education. Underlying the study of language and music is the assumption that the comparison of these two domains can shed light on the structural and functional properties of each, while also serving as a test case for theories of how the mind and, ultimately, the brain work. (...)
Brilliant Mistakes: Finding Success on the Far Side of Failure, Wharton Digital Press
Summary: If you have ever flown in an airplane, used electricity from a nuclear power plant, or taken an antibiotic, you have benefited from a brilliant mistake. Each of these life-changing innovations was the result of many missteps and an occasional brilliant insight that turned a mistake into a surprising portal of discovery. This book shares critical insights on the surprising benefits of making well-chosen mistakes. It explores why minimizing mistakes may be the greatest mistake of all, situations when mistakes are most beneficial and the counter-intuitive idea that we should deliberately permit errors at times. (...)
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Summary: The computational education of biologists is changing to prepare students for facing the complex datasets of today's life science research. In this concise textbook, the authors' fresh pedagogical approaches lead biology students from first principles towards computational thinking. A team of renowned bioinformaticians take innovative routes to introduce computational ideas in the context of real biological problems. Intuitive explanations promote deep understanding, using little mathematical formalism. Self-contained chapters show how computational procedures are developed and applied to central topics in bioinformatics and genomics, such as the genetic basis of disease, genome evolution or the tree of life concept. (...)
- Source: Bioinformatics for Biologists, Pavel Pevzner, Ron Shamir, Cambridge University Press, 2011/11/14
- Contributed by Anton Joha - antonjoha
gmail.com
Computational Complexity: Theory, Techniques, and Applications, Springer
Summary: Complex systems are systems that comprise many interacting parts with the ability to generate a new quality of collective behavior through self-organization, e.g. the spontaneous formation of temporal, spatial or functional structures. This book presents a detailed and integrated view of the theoretical basis, computational methods, and state-of-the-art approaches to investigating and modeling of inherently difficult problems whose solution requires extensive resources approaching the practical limits of present-day computer systems. This comprehensive and authoritative reference examines key components of computational complexity, including cellular automata, graph theory, data mining, granular computing, soft computing, wavelets, and more.
Links & Snippets
Other Publications
- Certain Interesting Properties of Action and Its Application Towards Achieving Greater Organization in Complex Systems, Atanu Bikash Chatterjee, 2011/11/14, arXiv:1111.3186
- Principle of Least Action and Theory of Cyclic Evolution, Atanu Bikash Chatterjee, 2011/11/18, arXiv:1111.5374
- Information processing reveals how microscopic components affect the macroscopic system-state in complex networks, Rick Quax, Andrea Apolloni, Peter M. A. Sloot, 2011/11/23, arXiv:1111.5483
Event Announcements
- The Dynamics of Disease, Workshop in Medical Systems Biology, Manchester, UK, 2011/11/28-12/02
- Network Frontier Workshop 2011, Evanston, IL, USA, 2011/12/01-02
- New England Complex Systems Institute Winter School, Cambridge, MA, USA, 2012/01/02-13
- 41th Winter Meeting on Statistical Physics, Xalapa, Veracruz, Mexico, 2012/01/3-6
- VI Congreso Bienal Internacional Complejidad 2012, Havana, Cuba, 2012/01/10-13
- 38th International Conference on Current Trends in Theory and Practice of Computer Science, Špindlerův Mlýn, Czech Republic, 2012/01/21-27
- 4th International Conference on Agents and Artificial Intelligence - ICAART 2012, Vilamoura, Algarve, Portugal, 2012/02/6-8
- WIVACE 2012 Italian Workshop on Artificial Life and Evolutionary Computation "Artificial Life, Evolution and Complexity" , Parma, Italy, 2012/02/20-21
- 3rd Workshop on Complex Networks, Melbourne, Florida, USA, 2012/03/7-9
- evostar - the main european events on evolutionary computation eurogp, evocop, evobio, evomusart and evoapplications, Málaga, Spain, 2012/03/11-13
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9th International Conference on the Evolution of Language (Evolang IX), Kyoto, Japan, 2012/03/13-16 - IWSOS'12 (Sixth International Workshop on Self-Organizing Systems), Delft, The Netherlands, 2012/03/15-16
- 5th International Nonlinear Science Conference 2012, Barcelona, Spain, 2011/03/15-17
- IPCAT 2012: Ninth International Conference on Information Processing in Cells and Tissues, Cambridge, United Kingdom, 2012/03/31-04/02
- 21st European Meeting on Cybernetics and Systems Research, Vienna, Austria, 2012/04/10-13
- Collective Intelligence 2012, Cambridge, MA, USA, 2012/04/18-20
- 2012 IEEE World Congress on Computational Intelligence, Brisbane, Australia, 2012/06/10-15
- CiE 2012 Turing Centenary conference: How the World Computes, Cambridge, UK, 2012/06/18-23
- GECCO 2012, Philadelphia, USA, 2012/07/7-11
- 25th European Conference on Operational Research, Vilnius, Lithuania, 2012/07/8-11
- ALife XIII: The Thirteenth International Conference on the Simulation and Synthesis of Living Systems, Lansig, Michigan, USA, 2012/08/19-22
- 12th International Conference on Parallel Problem Solving From Nature (PPSN2012), Taormina, Italy, 2012/09/1-5
- ECCS'12: European Conference on Complex Systems, Brussels, Belgium, 2012/09/3-7
- Interdisciplinary Symposium on Complex Systems, Kos island, Greece, 2012/09/19-25
Video Announcements
- Complexity Digest videos.
- Lakeside Labs videos.
- FuturICT videos.
- Brain-Mind Institute webinars
- IFISC@uib.es seminars.
- ASSYST Digital Library.
- TED Talks.
- Edge Videos
- CERN Webcast Service.
- Dean LeBaron's Video Casts.
Other Announcements
- Call for papers: Special issue of JSSC on Complex Systems and Sports, 2011/12/31
- ASSYSTComplexity
One of the main goals of the ASSYST Coordination Action is to promote Complex Systems for Socially Intelligent ICT (COSI-ICT) and, more generally, Complex Systems (CS) Science in Europe and Worldwide. We do this by communicating widely with scientists, policy makers, and business people, and by showcasing success stories of CS applications. - Job openings in Complex Systems
- Modelling and Physics of Complex Systems, MSc & PhD Programme, Universidad Rey Juan Carlos, Madrid, Spain.
- Research Positions in Complex Systems
The New England Complex Systems Institute (NECSI) has openings for postdoctoral appointments, and scholarships for research supervision in the study of complex systems. - Call for Papers: Cliodynamics: The Journal of Theoretical and Mathematical History
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Friends of Complexity Theory in Cuba, inlcudes Revista Pensando la Complejidad.
- DDLab, new release available! DDLab is a free set of tools for researching cellular automata, random Boolean networks, multi-value discrete dynamical networks, and beyond. See introductory video.
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